The Human Genome Project and the development of the expressed sequence tag (EST) clone collection and database have revolutionized gene expression analysis. Instead of measuring one or a few genes, parallel DNA microarrays are capable of simultaneously measuring expression of thousands of genes, providing a glimpse into the logic and functional grouping of gene programs encoded by our genome. The term functional genomics encompasses varied approaches that provide a more global investigation into the expression and role of groups of genes in a physiologic process than has been previously available. As such, this approach represents a fundamental shift from the traditional 'one gene at a time' approach to the study of basic biological processes. cDNA microarrays and oligonucleotide-based microarray methodologies have the potential to provide a new level of information about cell or tissue function not previously possible. However, these technologies require an investment in expensive equipment and highly trained, experienced technicians. Most laboratories cannot afford to commit the substantial technical resources and personnel to the development and ongoing refinement of these particularly complex experimental methods. It is more cost effective to concentrate this instrumentation and highly skilled technical support in a centrally managed facility, where they will be efficiently utilized and cost effective. The Functional Genomics Core Facility was designed to provide this critical core expertise to the digestive disease research community. The unique feature of the Functional Genomics Core Facility is the expertise it provides to participating investigators on the application of high density comprehensive arrays to study gastrointestinal and hepatic qene expression. In maintaining an independent microarray core, DDRCC research investigators are provided with access to the Agilent platforms at extremely low costs ($275/2 sample comparisons using the 44K gene arrays) and with much more rapid turn around time (<5 days) than other microarray facilities in the institution. The close proximity of the Functional Genomics Core to the DDRCC Morphology Core and the DDRCC Tissue Procurement Facility greatly facilitates the processing and analysis of clinical samples related to digestive disease disorders. The DDRCC Functional Genomics Core works closely with other microarray facilities at this institution that offer alternative commercial platforms, such as the Affymetrix platforms supported by the CTSA sponsored Translational Pathology and Tissue Banking Core, and the Illumina platforms supported by the Genome Sequencing Center of Washington University. Important for tight budgets, the cost of our services is less than half the cost of a single sample Affy array, and is about 20% less than the Illumina platform. Just as important, the Functional Genomics Core provides integrative and bioinformatic services.